Draw Lex et al.'s UpSet plots with Pandas and Matplotlib
Project description
This is another Python implementation of UpSet plots by Lex et al. [Lex2014].
It tries to provide a simple, interface backed by an extensible, object-oriented design.
The basic input format is a pandas.Series containing counts corresponding to set intersection sizes. The index indicates which rows pertain to which sets, by having multiple boolean indices, like example in the following:
>>> from upsetplot import generate_data
>>> example = generate_data(aggregated=True)
>>> example # doctest: +NORMALIZE_WHITESPACE
set0 set1 set2
False False False 56
True 283
True False 1279
True 5882
True False False 24
True 90
True False 429
True 1957
Name: value, dtype: int64
Then:
>>> from upsetplot import plot >>> plot(example) # doctest: +SKIP
makes:
Why an alternative to py-upset?
Probably for petty reasons. It appeared py-upset was not being maintained. Its input format was undocumented, inefficient and, IMO, inappropriate. It did not facilitate showing plots of each set intersection distribution as in Lex et al’s work introducing UpSet plots. Nor did it include the horizontal bar plots illustrated there. It did not support Python 2. I decided it would be easier to construct a cleaner version than to fix it.
References
Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis ‘14), vol. 20, no. 12, pp. 1983–1992, 2014. doi: doi.org/10.1109/TVCG.2014.2346248
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